Respiration and Photosynthesis: The Basics

First posted on 31/05/2022.

I am once again using this website as an Autism Loophole to force myself to do revision! So here's a summary of the chemical processes of photosynthesis and respiration that just so happens to line up with the OCR Biology A specification. Weird coincidence, huh?

So first off, what actually are they? Photosynthesis, in short, is the use of light energy to produce organic molecules, and respiration is the use of some respiratory substrate to produce energy in the form of ATP. Note that neither of these processes necessarily involve glucose, but in this summary I will be using glucose as an example.

Also, both photosynthesis and respiration rely on the electron transport chain. This is a collection of protein structures embedded in the inner membranes of the chloroplasts and mitochondria. High energy electrons move from protein to protein via funky quantum tunneling stuff. This energy is then used to pump protons across the membrane and establish a gradient. It is referred to by different names and is used for different things in each process, so keep an eye out for it!

Respiration

All respiration with glucose begins with glycolysis, which occurs in the cytoplasm. The first step of glycolysis is phosphorylation. 2 molecules of ATP donate a phosphate ion to the glucose, forming hexose bisphosphate. This molecule is unstable so it breaks down into two molecules of triose phosphate (lysis). Then, phosphorylation occurs again. However, this time the phosphate ions are inorganic and free-floating in the cytoplasm, so no ATP is required. This stage produces two molecules of triose bisphosphate. Four ATP molecules are then produced from the phosphate ions attached to the three-carbon compounds. From there, the triose bisphosphates are oxidised by NAD coenzymes (don't even worry about what those are, they're just kinda there) producing two molecules of pyruvate and two molecules of reduced NAD. This is an example of substrate level phosphorylation - the production of ATP without the involvement of the electron transport chain.

The net gain of glycolysis is 2 molecules of ATP, 2 molecules of reduced NAD and 2 molecules of pyruvate.

In aerobic respiration, the remaining reactions take place in the mitochondrial matrix. The next step is the link reaction, also known as oxidative decarboxylation. It's called that because our pyruvate is oxidised by NAD to form reduced NAD, and carbon dioxide is also removed. The resulting two-carbon acetyl group binds to coenzyme A (CoA) to form acetyl CoA. The acetyl group should properly be called an ethanoyl group but we're biologists so screw the proper chemistry.

From here, we begin the Krebs cycle. No, not the crab cycle. That's carcinization which I will probably do an infodump article on at some point. No, for now our acetyl group has been safely delivered so we can lose the CoA part. The acetyl group binds with 4 carbon oxaloacetate (OAA) to form 6 carbon citrate or citric acid. The citrate is then reduced by NAD producing reduced NAD and loses another carbon dioxide - dehydrogenation and decarboxylation. The resulting 5 carbon compound also undergoes dehydrogenation and decarboxylation in the same way. After that, ADP and inorganic phosphate bond to form a molecule of ATP. FAD, another coenzyme, then oxidises our now 4 carbon molecule to produce reduced FAD. FAD accepts two hydrogen atoms, incidentally. Before the cycle can repeat, one more hydrogen atom must be removed, turning another NAD into reduced NAD and then - would you look at that! We have our oxaloacetate back.

So far, we've made like 4 molecules of ATP and an absolute bunch of reduced coenzymes. So what are we going to do with all of them? This is where the electron transport chain comes back in.

This process can be called oxidative phosphorylation because it's producing ATP using oxygen, as opposed to substrate level phosphorylation which is anaerobic. The hydrogen atoms carried by our reduced coenzymes dissociate into hydrogen ions and high-energy excited electrons. These electrons power the electron transport chain as described at the beginning of this summary. So that gives us a proton gradient, with the intermembrane space in the mitochondria absolutely full of protons. The protons diffuse through a protein called ATP synthase, which uses this energy to build ATP. This little bit of the process is called chemiosmosis. Once the electrons reach the end of the electron transport chain, they combine with hydrogen ions and oxygen to make water. Oxygen is considered the final electron acceptor here.

Whew boy that was a lot huh? Well we're not done yet! What about when there's no oxygen around to accept those final electrons? The electron transport chain can't work under those circumstances, which is where anaerobic respiration comes in. It generally aims to keep glycolysis going so at least a little bit of ATP is produced.

There are plenty of different types of anaerobic respiration but I'm just going to go over fermentation here. But don't fret, there's different types of that too - alcoholic and lactate fermentation.

In anaerobic conditions, mammals undergo lactate fermentation. Pyruvate can accept hydrogen from reduced NAD, regenerating the NAD and turning into lactate (lactic acid). This allows glycolysis to continue, producing small amounts of ATP. The liver can then reclaim glucose from the lactic acid, but only in the presence of oxygen (hence the oxygen debt after exercise).

Fungi and some plants can carry out alcoholic fermentation. Pyruvate loses carbon dioxide and becomes ethanal, which then gains a hydrogen from reduced NAD and becomes ethanol. The NAD can then return to glycolysis. Unlike lactate, this process is irreversable.

So. Bloody hell that was a lot. Before we move on to photosynthesis, what else... Oh yeah, this process doesn't have to use glucose, it can use any number of respiratory substrates, which all have different efficiencies which can be measured using respiratory quotients (carbon dioxide produced over oxygen consumed). OK now go take a break.

Photosynthesis

Ok besties, snack break over. Photosynthesis can be divided into two reactions: Light dependent and light independent. Take a wild guess as to what differentiates them!

The light dependent stage is reliant on structures within the thylakoid membrane of the chloroplasts called photosystems. These are comprised of various pigments such as chlorophyll B, carotenoids and xanthophylls, as well as the primary pigment chlorophyll A. Each pigment picks up energy from a certain wavelength of light, which excites electrons. These electrons are then funnelled into the reaction centre where chlorophyll A is located.

These electrons are used to power electron transport chains in a process called photophosphorylation. Non-cyclic photophosphorylation starts off at a type of photosystem called photosystem II, which is a little silly but whatever let's roll with it. The excited electrons from PSII are passed down the electron transport chain, allowing chemiosmosis to occur and ATP to be produced. Yes, photosynthesis produces ATP. You were lied to. These electrons are then funneled into photosystem I where they get another boost of light for another run down the electron transport chain. This time, ATP is still produced but the electrons are accepted at the end by the coenzyme NADP, alongside a hydrogen ion, to form reduced NADP. It's just like NAD, but with a P for photosynthesis I guess.

But since this process is non-cyclic, how come PSII doesn't run out of electrons? This is where the process of photolysis comes in. Thanks to an enzyme, light splits water into hydrogen, oxygen and electrons. The electrons are used to refill PSII, oxygen gas is released as a byproduct and the hydrogen ions are released into the lumen of the thylakoid. This increases the concentration gradient and once they're done producing ATP they can be used to form reduced NADP at the end of non-cyclic photophosphorylation.

I can hear you thinking, so if there's non-cyclic photophosphorylation there has to be cyclic phosphorylation as well, right? And you're correct. Sometimes, instead of being used to form reduced NADP, the electrons at the end of PSI's electron transport chain just re-enter PSI and can be re-excited by light. While no reduced NADP is produced in this process, ATP still is.

Now, on to the light independent stage. This is called the Calvin cycle, not to be confused with the Krebs cycle or the crab cycle.

Carbon dioxide diffuses into the stroma of the chloroplasts and is combined with the 5 carbon compound ribulose bisphosphate (RuBP) using the enzyme RuBisCO. I'll talk more about this enzyme later because it's really funny. The unstable 6 carbon compound formed immediately breaks down into two 3 carbon glycerate 3-phosphate (GP) molecules. Each GP molecule is then converted into triose phosphate (hey remember that?) using an ATP and a reduced NADP each. These were produced in the light dependent stage. Most TP is used to regenerate the RuBP, which is a process you don't need to worry about. The remaining TP is then used to produce organic molecules such as glucose. To produce 1 glucose molecule, 6 carbon dioxides must enter the Calvin cycle and it must 'turn' 6 times. This produces 12 TP molecules, 2 of which are used to make the glucose. That's a total of 30 carbons, which makes 6 lots of 5 carbon RuBP compounts. That regenerates the cycle.

That's photosynthesis for you, but before you go let me regale you with how funny the existence of RuBisCO is. So, RuBisCO is supposed to stick carbon dioxide to RuBP in photosynthesis. RuBisCO is competitively inhibited by oxygen. Oxygen is a product of photosynthesis. The better it is at its job, the more it is inhibited. It sucks so bad that it is estimated to be the most abundant enzyme on Earth to make up for this fact. But it doesn't stop there! When RuBisCO is having fun sticking oxygen onto poor helpless RuBP molecules, it produces a molecule called 2-phosphoglycolate in a process called photorespiration. 2-PHOSPHOGLYCOLATE IS TOXIC. IT TAKES ATP TO REMOVE. The better RuBisCO gets at its job, the more it tries to kill the plant! This is one of many reasons I don't believe in intelligent design. If a god created RuBisCO, it must be either really stupid or treating this entire planet like a joke. Any kind of RuBisCO mutation will obviously kill the plant so it literally cannot evolve to be better. 25% of the products of photosynthesis are lost to RuBisCO's dumbassery. Think about how amazing plants could be with 25% more efficiency! If someone engineered a better RuBisCO they could immediately take over the world with plant-based annhialation. Adding that to the list of bioweapons I could totally build, you guys.

So that's pretty much it! I hope this was a little helpful for you. It sure was for me!

Love, Blue